Research workbench
Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole and phosphate in the T state
Analyse Complex of glycogen phosphorylase with a transition state analogue nojirimycin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NOJ
- Type
- protein
- Length
- 831 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, NTZ, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase (EC 2.4.1.1) | protein | 831 | 51% helix, 14% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NTZ · Nojirimycine tetrazole · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.83 | 0.95 | 41 | PO4, PLP, NTZ |
| 2 | 159 | 0.80 | 0.96 | 43 | empty |
| 3 | 358 | 0.67 | 0.81 | 38 | empty |
| 4 | 59 | 0.57 | 0.90 | 21 | empty |
| 5 | 114 | 0.55 | 0.83 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1NOJ · Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00489
- Elsewhere: RCSB PDB 1NOJ · PDBe 1NOJ · UniProt P00489
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